Mercurial > repos > jdv > albacore

comparison out_dir/configuration.cfg @ 8:3dfde840119e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
author jdv
date Mon, 18 Jun 2018 12:20:28 -0400
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7:ce1fa05ffb6c 8:3dfde840119e
1 [pipeline]
2 basecall_type = linear
3 min_qscore_1d = 7.0
4 desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_raw_basecall_1d.jsn
5 log_intermodule_messages = False
6
7 [data_trimmer]
8 ev_window = 20
9 ev_threshold = 5
10 min_events = 3
11 delta = 2
12 chunk_size_out = 0 # Use a nonzero value to chunk output
13
14 [basecaller]
15 model = template_r9.5_450bps_5mer_raw.jsn
16 implementation = auto
17 min_events = 100
18 max_events = 10000
19 overlap = 50
20 min_quality = -10.0
21 min_prob = 1e-5
22 simple_decoding = 1
23 homopolymer_correct = 0
24 model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned
25
26 [call_handler]
27 record_base = read
28 qscore_adjuster_intercept = 1.5
29 qscore_adjuster_slope = 1.5
30
31 [barcode_detector]
32
33 [fastq]
34 identifier = {read_id}
35 header = {identifier} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc}
36 header_with_barcoding = {identifier} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id}
37 batch_file_name = fastq_runid_{run_id}_{batch_counter}.{extension}
38 single_file_name = {read_id}.{extension}
39 all_file_name = fastq_runid_{run_id}.fastq
40
41 [fast5]
42 basecall_columns = mean,start,stdv,length,model_state,move,p_model_state,weights
43